Merge pull request #24 from cBioPortal/Fix-Core-Dep-Issues-And-CnaUtils

Fix core dep issues and cna utils

Author: haynescd

pom.xml

@@ -9,7 +9,7 @@
 
 	<groupId>org.mskcc.cbio</groupId>
 	<artifactId>core</artifactId>
-	<version>1.0.7-SNAPSHOT</version>
+	<version>1.0.7</version>
 
 	<name>Portal Core</name>
 	<description>Core libraries shared among other modules</description>

src/main/java/org/mskcc/cbio/portal/util/CnaUtil.java

@@ -53,14 +53,18 @@ public static void storeCnaEvents(
             if (!CNA.AMP.equals(cnaEvent.getAlteration()) && !CNA.HOMDEL.equals(cnaEvent.getAlteration())) {
                 continue;
             }
-            
-            CnaEvent.Event event = cnaEvent.getEvent();
-            if (existingCnaEvents.contains(event)) {
-                cnaEvent.setEventId(event.getEventId());
+
+            // Revert PR https://github.com/cBioPortal/cbioportal-core/pull/1 breaks importer
+            Optional<CnaEvent.Event> existingCnaEvent = existingCnaEvents
+                    .stream()
+                    .filter(e -> e.equals(cnaEvent.getEvent()))
+                    .findFirst();
+            if (existingCnaEvent.isPresent()) {
+                cnaEvent.setEventId(existingCnaEvent.get().getEventId());
                 DaoCnaEvent.addCaseCnaEvent(cnaEvent, false);
             } else {
                 DaoCnaEvent.addCaseCnaEvent(cnaEvent, true);
-                existingCnaEvents.add(event);
+                existingCnaEvents.add(cnaEvent.getEvent());
             }
         }
     }

src/main/resources/applicationContext-persistenceConnections.xml

@@ -27,6 +27,9 @@
             <property name="basePackage" value="org.mskcc.cbio.portal.persistence,org.cbioportal.persistence.mybatis" />
         </bean>
 
+
+        <bean id="cacheMapUtil" class="org.cbioportal.persistence.cachemaputil.InactiveCacheMapUtil" />
+
         <!-- enable component scanning (beware that this does not enable mapper scanning!) -->
         <context:component-scan base-package="org.mskcc.cbio.portal.util"/> <!-- - mainly to inject into global properties -->
         <context:component-scan base-package="org.cbioportal.persistence" />
@@ -35,6 +38,7 @@
         <!-- enable autowire -->
         <context:annotation-config />
 
+
         <!-- enable transaction demarcation with annotations -->
         <tx:annotation-driven />